The technically correct way would be to have the property management company report the income separately; one to you personally and one to the LLC.
Having said that, don't stress here. The end result will be the same since I assume you and your wife file a joint return.
What I would recommend is report all the income reported on the 1099 on the 1065. This will avoid a matching notice. Then reflect the income earned by the rental you own individually as an expense on the LLC return. Title this "income reported on individual rental" or something along those lines. Then make sure you report this "expense" as income on your 1040 Schedule E.
As stated previously, at the end of the day (end of preparing your tax return) all income and expense will be reported and the appropriate tax liability computed.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
